Three conservation groups and the N.C. Wildlife Resources Commission have agreed on new rules aimed at reducing the shooting deaths of endangered red wolves in five Eastern North Carolina counties by limiting the hunting of the wolves’ non-endangered lookalikes: coyotes.

In the five-county Red Wolf Recovery Area, nighttime hunting of coyotes will be banned, and special permits will be required for daytime hunting. The area is home to the world’s only wild red wolves, which have dwindled in recent years to an estimated count of 100.

The new rules are part of an agreement that settled a lawsuit by conservation groups accusing the Wildlife Resources Commission of violating the federal Endangered Species Act. The groups argued that by allowing coyote hunting, the state agency was responsible for the deaths of red wolves.

Hunting the wolves is illegal. But the animals are frequently mistaken for coyotes, and gunshot is the leading killer of red wolves.

“This settlement will advance the long-term protection of red wolves by reducing the likelihood that they will be killed by hunters who mistake them for coyotes, thereby facilitating species recovery,” said D.J. Schubert, wildlife biologist for the Washington-based Animal Welfare Institute, one of three plaintiffs in the lawsuit. “With only an estimated 100 red wolves remaining in the wild, each death by gunshot jeopardizes the survival of the species.”

Saving the wolves

The U.S. Fish and Wildlife Service has sought to reintroduce the red wolf with a program that started in 1987 at the Alligator River National Wildlife Refuge in Dare and Hyde counties. The red wolves’ gunshot death toll, 15 between 1987 and 2000, increased to 73 between 2000 and 2013.

The Wildlife Resources Commission has promoted trapping and hunting in recent years to reduce coyote attacks on livestock and pets. Across the state, hunters killed 27,000 coyotes last year.

A commission spokesman declined Thursday to comment on the new hunting rules or to say when they would take effect in the affected area: Dare, Hyde, Tyrrell, Beaufort and Washington counties.

The agreement was approved Wednesday in Elizabeth City by U.S. District Judge Terrence W. Boyle. The new hunting rules are a permanent replacement for a preliminary injunction Boyle issued in May, which temporarily halted all coyote hunting in the red wolf counties.

Under the new rules for the five counties:

—Coyote hunting remains illegal at night.

—Daytime hunting is legal only for licensed hunters, who also must have special coyote permits. Hunters must report coyote kills within 24 hours to the Wildlife Resources Commission.

—All coyote hunting permits in the five-county area will be suspended if two or more red wolves are shot during the same year on state game lands by hunters who have coyote permits.

After Boyle temporarily halted coyote hunting in the five-county area earlier this year, the Wildlife Resources Commission asked the Fish and Wildlife Service to reconsider its 27-year effort to restore red wolves. When the federal agency agreed to do so, it received more than 47,000 comments from citizens and organizations — including conservationists who support the program and Eastern North Carolina farmers who oppose it.

The Fish and Wildlife Service hired a nonprofit consulting group to evaluate the red wolf recovery program and to provide its recommendations by Friday. A decision is expected early next year.